data_3V3N
#
_model_server_result.job_id            -LCS5cV_fSECdty1T23nHA 
_model_server_result.datetime_utc      '2024-11-28 18:18:04' 
_model_server_result.server_version    0.9.12 
_model_server_result.query_name        ligand 
_model_server_result.source_id         pdb-bcif 
_model_server_result.entry_id          3v3n 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"I","auth_seq_id":2001}' 
#
_entry.id    3V3N 
#
_exptl.entry_id    3V3N 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              457.476 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '(4S,4AS,5AR,12AS)-4,7-BIS(DIMETHYLAMINO)-3,10,12,12A-TETRAHYDROXY-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2- CARBOXAMIDE' 
_entity.pdbx_number_of_molecules    4 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         111.11 
_cell.angle_beta          90.1 
_cell.angle_gamma         93.01 
_cell.entry_id            3V3N 
_cell.length_a            68.426 
_cell.length_b            80.102 
_cell.length_c            87.362 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3V3N 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 author_and_software_defined_assembly 2 
PISA monomeric 1 author_and_software_defined_assembly 3 
PISA monomeric 1 author_and_software_defined_assembly 4 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,E,F,G,H,U 1 1 
B,I,J,K,L,V 2 1 
C,M,N,O,P,W 3 1 
D,Q,R,S,T,X 4 1 
#
_pdbx_struct_oper_list.id                    1 
_pdbx_struct_oper_list.type                  'identity operation' 
_pdbx_struct_oper_list.name                  1_555 
_pdbx_struct_oper_list.symmetry_operation    x,y,z 
_pdbx_struct_oper_list.matrix[1][1]          1 
_pdbx_struct_oper_list.matrix[1][2]          0 
_pdbx_struct_oper_list.matrix[1][3]          0 
_pdbx_struct_oper_list.matrix[2][1]          0 
_pdbx_struct_oper_list.matrix[2][2]          1 
_pdbx_struct_oper_list.matrix[2][3]          0 
_pdbx_struct_oper_list.matrix[3][1]          0 
_pdbx_struct_oper_list.matrix[3][2]          0 
_pdbx_struct_oper_list.matrix[3][3]          1 
_pdbx_struct_oper_list.vector[1]             0 
_pdbx_struct_oper_list.vector[2]             0 
_pdbx_struct_oper_list.vector[3]             0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 E N N 
? 2 I N N 
? 2 M N N 
? 2 Q N N 
#
_chem_comp.formula           'C23 H27 N3 O7' 
_chem_comp.formula_weight    457.476 
_chem_comp.id                MIY 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '(4S,4AS,5AR,12AS)-4,7-BIS(DIMETHYLAMINO)-3,10,12,12A-TETRAHYDROXY-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2- CARBOXAMIDE' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     MINOCYCLINE 
#
loop_
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.comp_id
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_ordinal
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_aromatic_flag
O8 C21 MIY doub 328 n n 
C21 N2 MIY sing 329 n n 
C21 C2 MIY sing 330 n n 
N2 HN21 MIY sing 331 n n 
N2 HN22 MIY sing 332 n n 
C2 C1 MIY sing 333 n n 
C2 C3 MIY doub 334 n n 
C1 O1 MIY doub 335 n n 
C1 C18 MIY sing 336 n n 
C3 O2 MIY sing 337 n n 
C3 C4 MIY sing 338 n n 
O2 HO2 MIY sing 339 n n 
C4 N1 MIY sing 340 n n 
C4 C5 MIY sing 341 n n 
C4 H4 MIY sing 342 n n 
N1 C20 MIY sing 343 n n 
N1 C19 MIY sing 344 n n 
C20 H201 MIY sing 345 n n 
C20 H202 MIY sing 346 n n 
C20 H203 MIY sing 347 n n 
C19 H191 MIY sing 348 n n 
C19 H192 MIY sing 349 n n 
C19 H193 MIY sing 350 n n 
C5 C18 MIY sing 351 n n 
C5 C6 MIY sing 352 n n 
C5 H5 MIY sing 353 n n 
C18 O7 MIY sing 354 n n 
C18 C17 MIY sing 355 n n 
O7 HO7 MIY sing 356 n n 
C17 O6 MIY sing 357 n n 
C17 C16 MIY doub 358 n n 
O6 HO6 MIY sing 359 n n 
C16 C7 MIY sing 360 n n 
C16 C15 MIY sing 361 n n 
C7 C6 MIY sing 362 n n 
C7 C8 MIY sing 363 n n 
C7 H7 MIY sing 364 n n 
C6 H61 MIY sing 365 n n 
C6 H62 MIY sing 366 n n 
C15 O5 MIY doub 367 n n 
C15 C14 MIY sing 368 n n 
C14 C9 MIY doub 369 n y 
C14 C13 MIY sing 370 n y 
C9 C8 MIY sing 371 n n 
C9 C10 MIY sing 372 n y 
C8 H81 MIY sing 373 n n 
C8 H82 MIY sing 374 n n 
C13 O4 MIY sing 375 n n 
C13 C12 MIY doub 376 n y 
O4 HO4 MIY sing 377 n n 
C12 C11 MIY sing 378 n y 
C12 H12 MIY sing 379 n n 
C11 C10 MIY doub 380 n y 
C11 H11 MIY sing 381 n n 
C10 N7 MIY sing 382 n n 
N7 CN7 MIY sing 383 n n 
N7 C71 MIY sing 384 n n 
CN7 HN71 MIY sing 385 n n 
CN7 HN72 MIY sing 386 n n 
CN7 HN73 MIY sing 387 n n 
C71 H711 MIY sing 388 n n 
C71 H712 MIY sing 389 n n 
C71 H713 MIY sing 390 n n 
#
_atom_sites.entry_id                     3V3N 
_atom_sites.fract_transf_matrix[1][1]    0.014614 
_atom_sites.fract_transf_matrix[1][2]    0.000768 
_atom_sites.fract_transf_matrix[1][3]    0.000325 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.012501 
_atom_sites.fract_transf_matrix[2][3]    0.004835 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.012273 
_atom_sites.fract_transf_vector[1]       0 
_atom_sites.fract_transf_vector[2]       0 
_atom_sites.fract_transf_vector[3]       0 
#
loop_
_pdbx_nonpoly_scheme.asym_id
_pdbx_nonpoly_scheme.entity_id
_pdbx_nonpoly_scheme.mon_id
_pdbx_nonpoly_scheme.pdb_strand_id
_pdbx_nonpoly_scheme.ndb_seq_num
_pdbx_nonpoly_scheme.pdb_seq_num
_pdbx_nonpoly_scheme.auth_seq_num
_pdbx_nonpoly_scheme.pdb_mon_id
_pdbx_nonpoly_scheme.auth_mon_id
_pdbx_nonpoly_scheme.pdb_ins_code
E 2 MIY A 1 2001 2001 MIY MIY . 
F 3 SO4 A 1 2002 1 SO4 SO4 . 
G 3 SO4 A 1 2003 1 SO4 SO4 . 
H 4 FAD A 1 2004 1384 FAD FAD . 
I 2 MIY B 1 2001 2001 MIY MIY . 
J 3 SO4 B 1 2002 1 SO4 SO4 . 
K 3 SO4 B 1 2003 1 SO4 SO4 . 
L 4 FAD B 1 2004 1384 FAD FAD . 
M 2 MIY C 1 2001 2001 MIY MIY . 
N 3 SO4 C 1 2002 1 SO4 SO4 . 
O 3 SO4 C 1 2003 1 SO4 SO4 . 
P 4 FAD C 1 2004 1384 FAD FAD . 
Q 2 MIY D 1 2001 2001 MIY MIY . 
R 3 SO4 D 1 2002 1 SO4 SO4 . 
S 3 SO4 D 1 2003 1 SO4 SO4 . 
T 4 FAD D 1 2004 1384 FAD FAD . 
U 5 HOH A 1 2101 14 HOH HOH . 
U 5 HOH A 2 2102 21 HOH HOH . 
U 5 HOH A 3 2103 22 HOH HOH . 
U 5 HOH A 4 2104 29 HOH HOH . 
U 5 HOH A 5 2105 45 HOH HOH . 
U 5 HOH A 6 2106 51 HOH HOH . 
U 5 HOH A 7 2107 59 HOH HOH . 
U 5 HOH A 8 2108 66 HOH HOH . 
U 5 HOH A 9 2109 69 HOH HOH . 
U 5 HOH A 10 2110 90 HOH HOH . 
U 5 HOH A 11 2111 1 HOH HOH . 
U 5 HOH A 12 2112 2 HOH HOH . 
U 5 HOH A 13 2113 4 HOH HOH . 
U 5 HOH A 14 2114 1 HOH HOH . 
U 5 HOH A 15 2115 2 HOH HOH . 
U 5 HOH A 16 2116 3 HOH HOH . 
U 5 HOH A 17 2117 4 HOH HOH . 
U 5 HOH A 18 2118 5 HOH HOH . 
U 5 HOH A 19 2119 15 HOH HOH . 
U 5 HOH A 20 2120 22 HOH HOH . 
U 5 HOH A 21 2121 3 HOH HOH . 
U 5 HOH A 22 2122 4 HOH HOH . 
U 5 HOH A 23 2123 5 HOH HOH . 
U 5 HOH A 24 2124 7 HOH HOH . 
U 5 HOH A 25 2125 11 HOH HOH . 
U 5 HOH A 26 2126 12 HOH HOH . 
U 5 HOH A 27 2127 13 HOH HOH . 
U 5 HOH A 28 2128 14 HOH HOH . 
U 5 HOH A 29 2129 1 HOH HOH . 
V 5 HOH B 1 2101 4 HOH HOH . 
V 5 HOH B 2 2102 6 HOH HOH . 
V 5 HOH B 3 2103 7 HOH HOH . 
V 5 HOH B 4 2104 11 HOH HOH . 
V 5 HOH B 5 2105 16 HOH HOH . 
V 5 HOH B 6 2106 19 HOH HOH . 
V 5 HOH B 7 2107 20 HOH HOH . 
V 5 HOH B 8 2108 27 HOH HOH . 
V 5 HOH B 9 2109 35 HOH HOH . 
V 5 HOH B 10 2110 36 HOH HOH . 
V 5 HOH B 11 2111 37 HOH HOH . 
V 5 HOH B 12 2112 38 HOH HOH . 
V 5 HOH B 13 2113 41 HOH HOH . 
V 5 HOH B 14 2114 42 HOH HOH . 
V 5 HOH B 15 2115 43 HOH HOH . 
V 5 HOH B 16 2116 49 HOH HOH . 
V 5 HOH B 17 2117 54 HOH HOH . 
V 5 HOH B 18 2118 56 HOH HOH . 
V 5 HOH B 19 2119 60 HOH HOH . 
V 5 HOH B 20 2120 64 HOH HOH . 
V 5 HOH B 21 2121 70 HOH HOH . 
V 5 HOH B 22 2122 72 HOH HOH . 
V 5 HOH B 23 2123 74 HOH HOH . 
V 5 HOH B 24 2124 78 HOH HOH . 
V 5 HOH B 25 2125 86 HOH HOH . 
V 5 HOH B 26 2126 87 HOH HOH . 
V 5 HOH B 27 2127 88 HOH HOH . 
V 5 HOH B 28 2128 92 HOH HOH . 
V 5 HOH B 29 2129 93 HOH HOH . 
V 5 HOH B 30 2130 95 HOH HOH . 
V 5 HOH B 31 2131 1 HOH HOH . 
V 5 HOH B 32 2132 2 HOH HOH . 
V 5 HOH B 33 2133 17 HOH HOH . 
V 5 HOH B 34 2134 1 HOH HOH . 
V 5 HOH B 35 2135 4 HOH HOH . 
V 5 HOH B 36 2136 5 HOH HOH . 
V 5 HOH B 37 2137 7 HOH HOH . 
V 5 HOH B 38 2138 8 HOH HOH . 
V 5 HOH B 39 2139 9 HOH HOH . 
V 5 HOH B 40 2140 15 HOH HOH . 
V 5 HOH B 41 2141 16 HOH HOH . 
V 5 HOH B 42 2142 18 HOH HOH . 
V 5 HOH B 43 2143 19 HOH HOH . 
V 5 HOH B 44 2144 20 HOH HOH . 
V 5 HOH B 45 2145 21 HOH HOH . 
V 5 HOH B 46 2146 24 HOH HOH . 
V 5 HOH B 47 2147 25 HOH HOH . 
V 5 HOH B 48 2148 26 HOH HOH . 
V 5 HOH B 49 2149 2 HOH HOH . 
V 5 HOH B 50 2150 3 HOH HOH . 
W 5 HOH C 1 2101 1 HOH HOH . 
W 5 HOH C 2 2102 3 HOH HOH . 
W 5 HOH C 3 2103 9 HOH HOH . 
W 5 HOH C 4 2104 10 HOH HOH . 
W 5 HOH C 5 2105 15 HOH HOH . 
W 5 HOH C 6 2106 18 HOH HOH . 
W 5 HOH C 7 2107 23 HOH HOH . 
W 5 HOH C 8 2108 24 HOH HOH . 
W 5 HOH C 9 2109 25 HOH HOH . 
W 5 HOH C 10 2110 30 HOH HOH . 
W 5 HOH C 11 2111 34 HOH HOH . 
W 5 HOH C 12 2112 40 HOH HOH . 
W 5 HOH C 13 2113 44 HOH HOH . 
W 5 HOH C 14 2114 46 HOH HOH . 
W 5 HOH C 15 2115 55 HOH HOH . 
W 5 HOH C 16 2116 65 HOH HOH . 
W 5 HOH C 17 2117 76 HOH HOH . 
W 5 HOH C 18 2118 77 HOH HOH . 
W 5 HOH C 19 2119 80 HOH HOH . 
W 5 HOH C 20 2120 81 HOH HOH . 
W 5 HOH C 21 2121 85 HOH HOH . 
W 5 HOH C 22 2122 89 HOH HOH . 
W 5 HOH C 23 2123 94 HOH HOH . 
W 5 HOH C 24 2124 6 HOH HOH . 
W 5 HOH C 25 2125 1 HOH HOH . 
W 5 HOH C 26 2126 2 HOH HOH . 
W 5 HOH C 27 2127 4 HOH HOH . 
W 5 HOH C 28 2128 5 HOH HOH . 
W 5 HOH C 29 2129 6 HOH HOH . 
W 5 HOH C 30 2130 9 HOH HOH . 
W 5 HOH C 31 2131 10 HOH HOH . 
W 5 HOH C 32 2132 11 HOH HOH . 
W 5 HOH C 33 2133 13 HOH HOH . 
W 5 HOH C 34 2134 14 HOH HOH . 
W 5 HOH C 35 2135 16 HOH HOH . 
W 5 HOH C 36 2136 17 HOH HOH . 
W 5 HOH C 37 2137 18 HOH HOH . 
W 5 HOH C 38 2138 4 HOH HOH . 
W 5 HOH C 39 2139 5 HOH HOH . 
X 5 HOH D 1 2101 5 HOH HOH . 
X 5 HOH D 2 2102 8 HOH HOH . 
X 5 HOH D 3 2103 17 HOH HOH . 
X 5 HOH D 4 2104 26 HOH HOH . 
X 5 HOH D 5 2105 28 HOH HOH . 
X 5 HOH D 6 2106 32 HOH HOH . 
X 5 HOH D 7 2107 39 HOH HOH . 
X 5 HOH D 8 2108 48 HOH HOH . 
X 5 HOH D 9 2109 52 HOH HOH . 
X 5 HOH D 10 2110 53 HOH HOH . 
X 5 HOH D 11 2111 57 HOH HOH . 
X 5 HOH D 12 2112 61 HOH HOH . 
X 5 HOH D 13 2113 62 HOH HOH . 
X 5 HOH D 14 2114 63 HOH HOH . 
X 5 HOH D 15 2115 67 HOH HOH . 
X 5 HOH D 16 2116 73 HOH HOH . 
X 5 HOH D 17 2117 75 HOH HOH . 
X 5 HOH D 18 2118 83 HOH HOH . 
X 5 HOH D 19 2119 91 HOH HOH . 
X 5 HOH D 20 2120 6 HOH HOH . 
X 5 HOH D 21 2121 1 HOH HOH . 
X 5 HOH D 22 2122 2 HOH HOH . 
X 5 HOH D 23 2123 3 HOH HOH . 
X 5 HOH D 24 2124 4 HOH HOH . 
X 5 HOH D 25 2125 8 HOH HOH . 
X 5 HOH D 26 2126 9 HOH HOH . 
X 5 HOH D 27 2127 12 HOH HOH . 
X 5 HOH D 28 2128 13 HOH HOH . 
X 5 HOH D 29 2129 15 HOH HOH . 
X 5 HOH D 30 2130 17 HOH HOH . 
X 5 HOH D 31 2131 18 HOH HOH . 
X 5 HOH D 32 2132 6 HOH HOH . 
#
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_comp_id
_atom_site.label_seq_id
_atom_site.label_alt_id
_atom_site.pdbx_PDB_ins_code
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.pdbx_formal_charge
_atom_site.auth_atom_id
_atom_site.auth_comp_id
_atom_site.auth_seq_id
_atom_site.auth_asym_id
_atom_site.pdbx_PDB_model_num
HETATM 1 O O8 MIY . . . I 2 -16.045 9.58 -12.245 1 70.39 ? O8 MIY 2001 B 1 
HETATM 2 C C21 MIY . . . I 2 -16.75 10.048 -11.356 1 68.08 ? C21 MIY 2001 B 1 
HETATM 3 N N2 MIY . . . I 2 -16.941 9.413 -10.194 1 69.93 ? N2 MIY 2001 B 1 
HETATM 4 C C2 MIY . . . I 2 -17.399 11.35 -11.543 1 66.6 ? C2 MIY 2001 B 1 
HETATM 5 C C1 MIY . . . I 2 -18.516 11.701 -10.678 1 68.5 ? C1 MIY 2001 B 1 
HETATM 6 O O1 MIY . . . I 2 -18.683 11.211 -9.566 1 67.71 ? O1 MIY 2001 B 1 
HETATM 7 C C3 MIY . . . I 2 -16.992 12.224 -12.474 1 50.55 ? C3 MIY 2001 B 1 
HETATM 8 O O2 MIY . . . I 2 -16.201 11.82 -13.466 1 47.69 ? O2 MIY 2001 B 1 
HETATM 9 C C4 MIY . . . I 2 -17.388 13.681 -12.401 1 59.39 ? C4 MIY 2001 B 1 
HETATM 10 N N1 MIY . . . I 2 -17.358 14.342 -13.743 1 68.89 ? N1 MIY 2001 B 1 
HETATM 11 C C20 MIY . . . I 2 -17.692 15.764 -13.62 1 56.98 ? C20 MIY 2001 B 1 
HETATM 12 C C19 MIY . . . I 2 -18.298 13.765 -14.706 1 39.08 ? C19 MIY 2001 B 1 
HETATM 13 C C5 MIY . . . I 2 -18.671 13.94 -11.593 1 53.07 ? C5 MIY 2001 B 1 
HETATM 14 C C18 MIY . . . I 2 -19.476 12.704 -11.214 1 58.84 ? C18 MIY 2001 B 1 
HETATM 15 O O7 MIY . . . I 2 -20.191 12.153 -12.329 1 68.86 ? O7 MIY 2001 B 1 
HETATM 16 C C17 MIY . . . I 2 -20.47 12.938 -10.123 1 51.64 ? C17 MIY 2001 B 1 
HETATM 17 O O6 MIY . . . I 2 -21.403 12.013 -9.937 1 71.24 ? O6 MIY 2001 B 1 
HETATM 18 C C16 MIY . . . I 2 -20.448 13.995 -9.341 1 46.41 ? C16 MIY 2001 B 1 
HETATM 19 C C7 MIY . . . I 2 -19.514 15.123 -9.616 1 51.09 ? C7 MIY 2001 B 1 
HETATM 20 C C6 MIY . . . I 2 -18.276 14.589 -10.299 1 42.95 ? C6 MIY 2001 B 1 
HETATM 21 C C15 MIY . . . I 2 -21.388 14.046 -8.221 1 71.98 ? C15 MIY 2001 B 1 
HETATM 22 O O5 MIY . . . I 2 -22.201 13.145 -8.081 1 81.19 ? O5 MIY 2001 B 1 
HETATM 23 C C14 MIY . . . I 2 -21.359 15.24 -7.306 1 71.54 ? C14 MIY 2001 B 1 
HETATM 24 C C9 MIY . . . I 2 -20.176 16.127 -7.379 1 70.66 ? C9 MIY 2001 B 1 
HETATM 25 C C8 MIY . . . I 2 -19.045 15.77 -8.323 1 69.9 ? C8 MIY 2001 B 1 
HETATM 26 C C13 MIY . . . I 2 -22.46 15.608 -6.368 1 62.77 ? C13 MIY 2001 B 1 
HETATM 27 O O4 MIY . . . I 2 -23.592 14.843 -6.223 1 48.99 ? O4 MIY 2001 B 1 
HETATM 28 C C12 MIY . . . I 2 -22.315 16.764 -5.602 1 60.2 ? C12 MIY 2001 B 1 
HETATM 29 C C11 MIY . . . I 2 -21.2 17.592 -5.658 1 45.23 ? C11 MIY 2001 B 1 
HETATM 30 C C10 MIY . . . I 2 -20.125 17.333 -6.501 1 76.03 ? C10 MIY 2001 B 1 
HETATM 31 N N7 MIY . . . I 2 -19.013 18.211 -6.517 1 88.8 ? N7 MIY 2001 B 1 
HETATM 32 C CN7 MIY . . . I 2 -17.874 17.64 -5.774 1 69.95 ? CN7 MIY 2001 B 1 
HETATM 33 C C71 MIY . . . I 2 -19.378 19.489 -5.884 1 72.99 ? C71 MIY 2001 B 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    22 
_model_server_stats.query_time_ms           298 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           33 
#